Table 2. Thirty-eight SNPs associated with type 2 diabetes (T2D) risk and used to construct the T2D genetic score.
| Chr:Pos (hg19) | SNP (proxy) a | Locus | Effect/Other
Alleles (Proxy) |
Effect Allele
Frequency (Proxy) b |
Beta c | Source in which SNP was
originally identified |
|---|---|---|---|---|---|---|
| 1:120526982 | rs1493694 | NOTCH2 | T/C | 0.11 | 0.110 | Zeggini et al., 2008 27 |
| 1:214163675 | rs340835 | PROX1 | A/G | 0.49 | 0.062 | Dupuis et al., 2010 9 |
| 2:27741237 | rs780094 | GCKR | C/T | 0.62 | 0.011 | Dupuis et al., 2010 9 |
| 2:43732823 | rs7578597 | THADA | T/C | 0.89 | 0.141 | Zeggini et al., 2008 27 |
| 2:60584819 | rs243021 | BCL11A | A/G | 0.46 | 0.090 | Voight et al., 2010 26 |
| 2:227093745 | rs2943641
(rs2943640) |
IRS1 | C/T
(C/A) |
0.65
(0.65) |
0.083 | Rung et al., 2009 28 |
| 3:12393125 | rs1801282 | PPARG | C/G | 0.88 | 0.138 | Altshuler et al., 2000 29 |
| 3:23336450 | rs7612463 | UBE2E2 | C/A | 0.89 | 0.102 | Yamauchi et al., 2010 30 |
| 3:64711904 | rs4607103
(rs6795735) |
ADAMTS9 | C/T
(C/T) |
0.76
(0.59) |
0.092 | Zeggini et al., 2008 27 |
| 3:123065778 | rs11708067
(rs2877716) |
ADCY5 | A/G
(C/T) |
0.75
(0.73) |
0.097 | Dupuis et al., 2010 9 |
| 4:6292915 | rs10010131 | WFS1 | G/A | 0.60 | 0.104 | Sandhu et al., 2007 31 |
| 5:76424949 | rs4457053 | ZBED3 | G/A | 0.32 | 0.150 | Voight et al., 2010 26 |
| 6:20661250 | rs7754840
(rs9368222) |
CDKAL1 | C/G
(A/C) |
0.31
(0.26) |
0.170 | Zeggini et al., 2007 32 |
| 7:28189411 | rs1635852 | JAZF1 | T/C | 0.49 | 0.120 | Zeggini et al., 2008 27 |
| 7:44235668 | rs4607517
(rs1799884) |
GCK | A/G
(T/C) |
0.18
(0.18) |
0.029 | Dupuis et al., 2010 9 |
| 7:130466854 | rs972283
(rs4731702) |
KLF14 | G/A
(C/T) |
0.51
(0.51) |
0.099 | Kong et al., 2009 33 |
| 8:95937502 | rs7845219 | TP53INP1 | T/C | 0.50 | 0.093 | Voight et al., 2010 4 |
| 8:118184783 | rs13266634 | SLC30A8 | C/T | 0.69 | 0.139 | Sladek et al., 2007 34 |
| 9:22133284 | rs10965250 | CDKN2A/B | G/A | 0.83 | 0.181 | Zeggini et al., 2007 32 |
| 9:81952128 | rs13292136 | CHCHD9 | C/T | 0.93 | 0.182 | Voight et al., 2010 26 |
| 10:12328010 | rs12779790
(rs11257655) |
CDC123/ CAMK1D | G/A
(T/C) |
0.18
(0.21) |
0.088 | Zeggini et al., 2008 27 |
| 10:94465559 | rs5015480 | HHEX/IDE | C/T | 0.59 | 0.166 | Zeggini et al., 2007 32 |
| 10:114758349 | rs7903146 | TCF7L2 | T/C | 0.29 | 0.335 | Grant et al., 2006 35 |
| 11:1696849 | rs2334499 | HCCA2/DUSP8 | T/C | 0.42 | 0.080 | Kong et al., 2009 33 |
| 11:2691471 | rs231362 | KCNQ1 | G/A | 0.52 | 0.104 | Kong et al., 2009 33 |
| 11:2847069 | rs163184 | KCNQ1 | G/T | 0.48 | 0.083 | Yasuda
et al., 2008
36, Unoki
et al., 2008 37 |
| 11:17408630 | rs5215 | KCNJ11 | C/T | 0.36 | 0.089 | Gloyn et al., 2003 38 |
| 11:72433098 | rs1552224 | CENTD2 | A/C | 0.84 | 0.123 | Voight et al., 2010 26 |
| 11:92673828 | rs1387153
(rs10830963) |
MTNR1B | T/C
(G/C) |
0.29
(0.28) |
0.115 | Prokopenko
et al., 2009
39,
Dupuis et al., 2010 9 |
| 12:66170163 | rs2612067 | HMGA2 | G/T | 0.10 | 0.180 | Voight et al., 2010 26 |
| 12:71613276 | rs1353362 | TSPAN8/ LGR5 | C/T | 0.28 | 0.103 | Zeggini et al., 2008 27 |
| 12:121402932 | rs7305618
(rs12427353) |
HNF1A | C/T
(G/C) |
0.77
(0.81) |
0.112 | Voight et al., 2010 26 |
| 13:80717156 | rs1359790 | SPRY2 | G/A | 0.71 | 0.096 | Shu et al., 2010 40 |
| 15:62396389 | rs7172432 | C2CD4A/B | A/G | 0.57 | 0.068 | Yamauchi et al., 2010 30 |
| 15:77747190 | rs7178572 | HMG20A | G/A | 0.71 | 0.068 | Kooner et al., 2011 41 |
| 15:80432222 | rs11634397 | ZFAND6 | G/A | 0.66 | 0.102 | Voight et al., 2010 26 |
| 17:36098040 | rs4430796 | HNF1B | G/A | 0.48 | 0.130 | Gudmundsson et al., 2007 42 |
| X:152908152 | rs2301142 | DUSP9 | A/G | 0.85 | 0.086 | Voight et al., 2010 26 |
SNP, single nucleotide polymorphism. aProxy SNPs were genotyped and analysed in the Hyperglycemia and Adverse Pregnancy Outcome Study (r 2 > 0.7 in 340,000 British white unrelated samples from Version 3 release of UK Biobank 24, except for at ADAMTS9 where r 2 = 0.45 24, calculated using PLINK software 25). bEffect allele frequency was calculated in 340,000 British white unrelated samples from the UK Biobank 24. cBeta values were aligned to the T2D-risk allele on the + strand (Human Genome Assembly Reference hg19). Beta value = log odds ratio for T2D from genome-wide association study meta-analysis of up to 8130 cases and 38987 controls, published in Voight et al. 2010 26. We used the same Beta value for proxy SNPs. We excluded rs8042680 ( PRC1 locus, Atlantic Diabetes in Pregnancy Study) and rs1470579 ( IGF2BP2 locus, Hyperglycemia and Adverse Pregnancy Outcome Study) from the T2D GS due to deviation from Hardy-Weinberg Equilibrium (Bonferroni-corrected P <0.05). We additionally excluded rs11642841 ( FTO locus) due to its primary effect on BMI 23.